\(\sum{(Px(value==1)*px\_resolution ^2 )}\)
library(pixmap)
library(magrittr)
library(EBImage)
library(image.LineSegmentDetector)
library(image.ContourDetector)
library(image.CannyEdges)
setwd("~/Zellkraftwerk/packages/RJobTissueArea")
file <- file.path("inst/data","data_sum_M1730408_pos11.csv")
data.sum <- file%>%
data.table::fread()
m.data_sum <- data.sum%>%
as.matrix()
#cellres: pixel resolution in horizontal and vertical direction
image <-pixmapGrey(m.data_sum,cellres=c(1,1))
plot(image)
EBImage
constant threshold
grid <- expand.grid(
sigma = seq(0.5,3,0.4),
threshold = seq(2,4,0.25)
)
grid$min <- NA
grid$max <- NA
img2 <- image@grey * 255
# Set up plots for 96 dpi images
#library(EBImage)
#dm <- dim(img2)/96
#dev.new(width = dm[1], height = dm[2])
# Low pass filter with gblur and make binary
par(mfrow=c(1,2))
for(i in 1:dim(grid)[1]){
writeLines(c(
paste0("- sigma: ",grid$sigma[i]),
paste0("- threshold: ", grid$threshold[i])
))
#Low-pass Gaussian filter
xb <- EBImage::gblur(img2, grid$sigma[i])
xb <- round(xb,digits = 0)
#plot(xb)
image2 <- pixmapGrey(xb,cellres=c(1,1)) #(xb-min(xb))/(max(xb)-min(xb))
plot(image2)
grid$min[i] <- min(xb)
grid$max[i] <- max(xb)
#threshold filtering
pos <- which(xb > grid$threshold[i])
xt <- xb
xt[which(xb > grid$threshold[i])] <- 1
xt[which(xb <= grid$threshold[i])] <- 0
#xt <- EBImage::thresh(xb, w=grid$w[i],
# h=grid$w[i],
# offset = grid$offset[i])
#plot(xt)
image3 <- image
image3@grey <- xt
plot(image3)
}## - sigma: 0.5
## - threshold: 2
## - sigma: 0.9
## - threshold: 2
## - sigma: 1.3
## - threshold: 2
## - sigma: 1.7
## - threshold: 2
## - sigma: 2.1
## - threshold: 2
## - sigma: 2.5
## - threshold: 2
## - sigma: 2.9
## - threshold: 2
## - sigma: 0.5
## - threshold: 2.25
## - sigma: 0.9
## - threshold: 2.25
## - sigma: 1.3
## - threshold: 2.25
## - sigma: 1.7
## - threshold: 2.25
## - sigma: 2.1
## - threshold: 2.25
## - sigma: 2.5
## - threshold: 2.25
## - sigma: 2.9
## - threshold: 2.25
## - sigma: 0.5
## - threshold: 2.5
## - sigma: 0.9
## - threshold: 2.5
## - sigma: 1.3
## - threshold: 2.5
## - sigma: 1.7
## - threshold: 2.5
## - sigma: 2.1
## - threshold: 2.5
## - sigma: 2.5
## - threshold: 2.5
## - sigma: 2.9
## - threshold: 2.5
## - sigma: 0.5
## - threshold: 2.75
## - sigma: 0.9
## - threshold: 2.75
## - sigma: 1.3
## - threshold: 2.75
## - sigma: 1.7
## - threshold: 2.75
## - sigma: 2.1
## - threshold: 2.75
## - sigma: 2.5
## - threshold: 2.75
## - sigma: 2.9
## - threshold: 2.75
## - sigma: 0.5
## - threshold: 3
## - sigma: 0.9
## - threshold: 3
## - sigma: 1.3
## - threshold: 3
## - sigma: 1.7
## - threshold: 3
## - sigma: 2.1
## - threshold: 3
## - sigma: 2.5
## - threshold: 3
## - sigma: 2.9
## - threshold: 3
## - sigma: 0.5
## - threshold: 3.25
## - sigma: 0.9
## - threshold: 3.25
## - sigma: 1.3
## - threshold: 3.25
## - sigma: 1.7
## - threshold: 3.25
## - sigma: 2.1
## - threshold: 3.25
## - sigma: 2.5
## - threshold: 3.25
## - sigma: 2.9
## - threshold: 3.25
## - sigma: 0.5
## - threshold: 3.5
## - sigma: 0.9
## - threshold: 3.5
## - sigma: 1.3
## - threshold: 3.5
## - sigma: 1.7
## - threshold: 3.5
## - sigma: 2.1
## - threshold: 3.5
## - sigma: 2.5
## - threshold: 3.5
## - sigma: 2.9
## - threshold: 3.5
## - sigma: 0.5
## - threshold: 3.75
## - sigma: 0.9
## - threshold: 3.75
## - sigma: 1.3
## - threshold: 3.75
## - sigma: 1.7
## - threshold: 3.75
## - sigma: 2.1
## - threshold: 3.75
## - sigma: 2.5
## - threshold: 3.75
## - sigma: 2.9
## - threshold: 3.75
## - sigma: 0.5
## - threshold: 4
## - sigma: 0.9
## - threshold: 4
## - sigma: 1.3
## - threshold: 4
## - sigma: 1.7
## - threshold: 4
## - sigma: 2.1
## - threshold: 4
## - sigma: 2.5
## - threshold: 4
## - sigma: 2.9
## - threshold: 4
grid## sigma threshold min max
## 1 0.5 2.00 0 203
## 2 0.9 2.00 0 201
## 3 1.3 2.00 0 194
## 4 1.7 2.00 0 185
## 5 2.1 2.00 0 174
## 6 2.5 2.00 0 163
## 7 2.9 2.00 0 151
## 8 0.5 2.25 0 203
## 9 0.9 2.25 0 201
## 10 1.3 2.25 0 194
## 11 1.7 2.25 0 185
## 12 2.1 2.25 0 174
## 13 2.5 2.25 0 163
## 14 2.9 2.25 0 151
## 15 0.5 2.50 0 203
## 16 0.9 2.50 0 201
## 17 1.3 2.50 0 194
## 18 1.7 2.50 0 185
## 19 2.1 2.50 0 174
## 20 2.5 2.50 0 163
## 21 2.9 2.50 0 151
## 22 0.5 2.75 0 203
## 23 0.9 2.75 0 201
## 24 1.3 2.75 0 194
## 25 1.7 2.75 0 185
## 26 2.1 2.75 0 174
## 27 2.5 2.75 0 163
## 28 2.9 2.75 0 151
## 29 0.5 3.00 0 203
## 30 0.9 3.00 0 201
## 31 1.3 3.00 0 194
## 32 1.7 3.00 0 185
## 33 2.1 3.00 0 174
## 34 2.5 3.00 0 163
## 35 2.9 3.00 0 151
## 36 0.5 3.25 0 203
## 37 0.9 3.25 0 201
## 38 1.3 3.25 0 194
## 39 1.7 3.25 0 185
## 40 2.1 3.25 0 174
## 41 2.5 3.25 0 163
## 42 2.9 3.25 0 151
## 43 0.5 3.50 0 203
## 44 0.9 3.50 0 201
## 45 1.3 3.50 0 194
## 46 1.7 3.50 0 185
## 47 2.1 3.50 0 174
## 48 2.5 3.50 0 163
## 49 2.9 3.50 0 151
## 50 0.5 3.75 0 203
## 51 0.9 3.75 0 201
## 52 1.3 3.75 0 194
## 53 1.7 3.75 0 185
## 54 2.1 3.75 0 174
## 55 2.5 3.75 0 163
## 56 2.9 3.75 0 151
## 57 0.5 4.00 0 203
## 58 0.9 4.00 0 201
## 59 1.3 4.00 0 194
## 60 1.7 4.00 0 185
## 61 2.1 4.00 0 174
## 62 2.5 4.00 0 163
## 63 2.9 4.00 0 151write.csv(grid,"grid_resulttable.csv")supplement
adapting threshold
grid <- expand.grid(sigma = c(1,2,3,4,5,10,100),
offset = c(100,10,1,0,0.01,0.001,0.0001,0.00001,0.000001,0.0000001),
w=c(1,5,10,50))
img2 <- image@grey * 255
# Set up plots for 96 dpi images
#library(EBImage)
#dm <- dim(img2)/96
#dev.new(width = dm[1], height = dm[2])
# Low pass filter with gblur and make binary
for(i in 1:dim(grid)[1]){
writeLines(c(
paste0("- sigma: ",grid$sigma[i]),
paste0("- offset: ", grid$offset[i]),
paste0(" - w and h: ",grid$w[i])
))
#Low-pass Gaussian filter
xb <- EBImage::gblur(img2, grid$sigma[i])
plot(xb)
image2 <- pixmapGrey(xb,cellres=c(1,1)) #(xb-min(xb))/(max(xb)-min(xb))
plot(image2)
xt <- EBImage::thresh(xb, w=grid$w[i],
h=grid$w[i],
offset = grid$offset[i])
plot(xt)
image3 <- image
image3@grey <- xt
plot(image3)
}image_line_segment_detector
x <- image@grey * 255
linesegments <- image_line_segment_detector(x,
scale = 0.8,
sigma_scale = 0.6,
quant = 2,
ang_th = 22.5,
log_eps = 0,
density_th = 0.7,
n_bins = 1024,
union = FALSE,
union_min_length = 5,
union_max_distance = 5,
union_ang_th = 7,
union_use_NFA = FALSE,
union_log_eps = 0)
linesegments
plot(image)
plot(linesegments, add = TRUE, col = "red")image_contour_detector
contourlines <- image_contour_detector(x, Q = 2)
contourlines
plot(image)
plot(contourlines, add = TRUE, col = "red")image_canny_edge_detector
edges <- image_canny_edge_detector(x)
edges
plot(edges)